At the end of the year, Binotto will step down as team principal.
The process to find a replacement for the 53-year-old had begun, according to a statement from the company.
Binotto said that he had decided to end his collaboration with Ferrari.
As hard as this decision has been for me, it is the right thing to do.
Binotto worked his way up through the company and eventually became the technical director of the F1 team.
He leaves at the end of the season in which Ferrari achieved their goals of returning to winning races but which was marked by a number of reliability failures and operational errors.
Binotto said that he was leaving a company that he loved and that he had made every effort to achieve the objectives.
I'm leaving a growing team. I wish all the best for the future because I believe a strong team will achieve the highest goals.
Benedetto Vigna thanked Binotto and said that the team was in a good position to win the ultimate prize.
Frederic Vasseur is said to be Binotto's replacement.
Two weeks ago, the company described reports in Italy that Binotto was going to leave the team and be replaced by Vasseur as "total without foundation".
Binotto didn't seem to want to leave his position at the grand prix.
He said that he and the chairman of Ferrari had talked openly about what was the best way to move forward and that he decided to release a statement that was perhaps the best way to close the speculation.
Binotto was going to leave and Vasseur was going to take his place. The "speculation" has proven to be correct.
Binotto paid the price for not addressing the weaknesses of the team. He achieved his goal of returning the team to competitiveness, but it wasn't enough as Ferrari missed out on their first winning car in over a year.
Charles Leclerc led Max Verstappen by 46 points after the third race of the season. The Red Bull driver was in front after three races.
In the spring and summer, Leclerc's campaign was destroyed. The team lost the victory in Monaco when they bungled their strategy after engine failures in Spain and Azerbaijan.
Two more wins were lost due to race-management errors. Red Bull moved ahead in car development in the second half of the season, while errors continued to plague Ferrari.
The environment of fear that many believe stifles creativity and brave decisions at the team was one of the reasons Binotto tried to instill a no-blame culture.
Despite that, there wasn't much progress in resolving the team's inherent problems.
The purpose of a no-blame culture is to create an environment of responsibility and trust that allows issues to be identified, understood and solved without those involved fearing for their jobs. Despite the repeated errors, nothing appeared to change.
One of the stars of the new generation of drivers, Charles Leclerc, seems to have lost his patience due to the mistakes. Fear of losing the Monegasque to Mercedes in the future is one of the reasons for this decision.
Questionable race strategy and a failure to keep up with the development of rivals such as Mercedes and Red Bull have been recurring themes for a decade and more.
If Vasseur does join, he will join the team with a reputation for being a race-team leader. He has been a boss of two teams, but he has never had a job like this.
It will take more than Vasseur's relationship with Leclerc to turn the team into a contender for the F1 title.